Evaluating robustness of a diesel-degrading bacterial consortium isolated from contaminated soil

Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments

The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.

Bacterial Diversity in Old Hydrocarbon Polluted Sediments of Ecuadorian Amazon River Basins

The Ecuadorian Amazon rainforest stands out as one of the world's most biodiverse regions, yet faces significant threats due to oil extraction activities dating back to the 1970s in the northeastern provinces. This research investigates the environmental and societal consequences of prolonged petroleum exploitation and oil spills in Ecuador's Amazon. Conducted in June 2015, the study involved a comprehensive analysis of freshwater sediment samples from 24 locations in the Rio Aguarico and Napo basins. Parameters such as water and air temperature, conductivity, soil pH, and hydrocarbon concentrations were examined. Total petroleum hydrocarbon (TPH) concentrations ranged from 9.4 to 847.4 mg kg-1, with polycyclic aromatic hydrocarbon (PAH) levels varying from 10.15 to 711.1 mg kg-1. The pristane/phytane ratio indicated historic hydrocarbon pollution in 8 of the 15 chemically analyzed sediments. Using non-culturable techniques (Illumina), bacterial analyses identified over 350 ASV, with prominent families including Comamonadaceae, Chitinophagaceae, Anaeromyxobacteraceae, Sphingomonadaceae, and Xanthobacteraceae. Bacterial diversity, assessed in eight samples, exhibited a positive correlation with PAH concentrations. The study provides insights into how microbial communities respond to varying levels of hydrocarbon pollution, shedding light on the enduring impact of oil exploitation in the Amazonian region. Its objective is to deepen our understanding of the environmental and human well-being in the affected area, underscoring the pressing need for remedial actions in the face of ongoing ecological challenges.

2,4-D versus 2,4-D based ionic liquids: Effect of cation on herbicide biodegradation, tfdA genes abundance and microbiome changes during soil bioaugmentation

The commercial formulations of herbicides rely on surfactants which increase the efficiency of active substance. Herbicidal ionic liquids (ILs), in which cationic surfactants are combined with herbicidal anions, allow for additives' reduction and ensure very good herbicide performance with lower doses. We aimed to test the impact of synthetic and natural cations on biological degradation of 2,4-dichlorophenoxyacetic acid (2,4-D). Although primary biodegradation was high, the mineralization in agricultural soil indicated incomplete conversion of ILs to CO₂. Even the introduction of naturally-derived cations resulted in an increase in the herbicide's half-lives - from 32 days for [Na][2,4-D] to 120 days for [Chol][2,4-D] and 300 days for the synthetic tetramethylammonium derivative [TMA][2,4-D]. Bioaugmentation with 2,4-D-degrading strains improves the herbicides' degradation, which was reflected by higher abundance of tfdA genes. Microbial community analysis confirmed that hydrophobic cationic surfactants, even those based on natural compounds, played a negative role on microbial biodiversity. Our study provides a valuable indication for further research related to the production of a new generation of environmentally friendly compounds. Moreover, the results shed a new light on the ionic liquids as independent mixtures of ions in the environment, as opposed to treating them as new type of environmental pollutants.

Construction of bifunctional bacterial community for co-contamination remediation: Pyrene biodegradation and cadmium biomineralization

Polycyclic aromatic hydrocarbons and heavy metals are typical pollutants in the non-ferrous metal smelting industry. The combination of biodegradation and biomineralization has great development potential for co-contamination removal as an environmentally friendly method. Pyrene (Pyr) and cadmium (Cd) were regarded as model pollutants of co-contamination in this study. A bifunctional bacterial community named Ycp was screened from a non-ferrous smelting slag field soil. The 16S rRNA gene high throughput sequencing analysis showed that Enterobacter was the dominant genus (99.1%). Ycp had adaptability under a wide range of environmental conditions (pH 3-9, salinity 0-10 g L^-1 NaCl, Pyr concentration 0-50 mg L^-1, Cd concentration 0-100 mg L^-1), and the removal rate of Pyr and Cd reached 41.8%-76.9%, 82.8%-98.8%, respectively. It was found that compound carbon sources had promoting effect on the removal of Pyr and Cd, with the maximum removal rate of 88.3% and 98.0%. According to the degradation products of Pyr by LC-MS analysis and the mineralized products of Cd²⁺ by XRD and SEM-EDS analysis, the mechanism of Ycp for co-contamination remediation was: Ycp biodegraded Pyr through salicylic acid and phthalic acid metabolic pathways, and biomineralized Cd²⁺ into CdCO₃ through microbially induced carbonate precipitation. This study provided a basis for microbial remediation of co-contamination.

Temporal compositional shifts in an activated sludge microbiome during estrone biodegradation

Microbial biodegradation is a key process for the removal of estrogens during wastewater treatment. At least four degradation pathways for natural estrogens have been proposed. However, major estrogen degraders and the occurrence of different estrogen biodegradation pathways in wastewater treatment plants have been rarely investigated. This study was conducted to elucidate estrone biodegradation pathway and to identify key estrone-degrading bacteria in activated sludge from a major wastewater treatment plant in Bahrain. The biodegradation experiments were performed in activated sludge microcosms supplemented with estrone. Sludge samples were retrieved at time intervals to analyze the biodegradation metabolites and the temporal shifts in the bacterial community composition. Chemical analysis revealed the biodegradation of more than 90% of the added estrone within 6 days, and the compounds 4-hydroxyestrone and pyridinestrone acid, which are typical markers of the 4,5-seco pathway of aerobic estrone biodegradation, were detected. Temporal shifts in the relative abundance of bacteria were most prominent among members of Proteobacteria and Bacteroidetes. While the alphaproteobacterial genera Novosphingobium and Sphingoaurantiacus were significantly enriched (from ≤ 6% to an average of 31%) in the estrone-amended activated sludge after 2 days of incubation, the bacteroidete Pedobacter was uniquely detected in these microcosms at day 10. The relative abundance of Polyangia (Nannocyctis) increased to an average of 10 ± 0.4% in the estrone-amended activated sludge after 4 days of incubation. Enrichment cultivation of bacteria from the activated sludge on estrone resulted in a mixed culture that was capable of degrading estrone. An estrone-degrading strain was isolated from this mixed culture and was affiliated with the known estrogen-degrading Alphaproteobacteria Sphingobium estrogenivorans. We conclude that estrone degradation in the activated sludge from the studied wastewater treatment plant proceeds via the 4,5-seco pathway and is most likely mediated by alphaproteobacterial taxa.

The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel

Bioprospecting of microorganisms suitable for bioremediation of fuel or oil spills is often carried out in contaminated environments such as gas stations or polluted coastal areas. Using next-generation sequencing (NGS) we analyzed the microbiota thriving below the lids of the fuel deposits of diesel and gasoline cars. The microbiome colonizing the tank lids differed from the diversity found in other hydrocarbon-polluted environments, with Proteobacteria being the dominant phylum and without clear differences between gasoline or diesel-fueled vehicles. We observed differential growth when samples were inoculated in cultures with gasoline or diesel as the main carbon source, as well as an increase in the relative abundance of the genus Pseudomonas in diesel. A collection of culturable strains was established, mostly Pseudomonas, Stenotrophomonas, Staphylococcus, and Bacillus genera. Strains belonging to Bacillus, Pseudomonas, Achromobacter, and Isoptericola genera showed a clear diesel degradation pattern when analyzed by GC-MS, suggesting their potential use for bioremediation and a possible new species of Isoptericola was further characterized as hydrocarbon degrader.

Soil microbial community responses to the application of a combined amendment in a historical zinc smelting area

Farmland soils that surround a historical zinc smelting area in northwestern Guizhou, China, are characterized by high levels of heavy metal accumulation. Previous studies have mainly focused on the potential risk evaluations of heavy metals in soil and crops. However, at present, the effects of amendment applications on the bioavailability of heavy metals and on microbial community in the heavily contaminated soils of the mining region are still unclear. A pot experiment was conducted to determine the effect of applying a combined amendment (e.g. lime, sepiolite, and vermicompost) on the diversity and composition of microbial community in the contaminated soil. The results showed that the contents of DTPA- and TCLP-extractable heavy metals (e.g. Cd, Pb, and Zn) decreased and that the pH, SWC, EC, and soil available nutrient (e.g. AN, AP, and AK) contents increased after the application of the combined amendment. Furthermore, application of the combined amendment decreased the diversity of soil bacterial and fungal communities and increased the relative abundances of the dominant bacterial and fungal communities such as Proteobacteria, Bacteroidetes, and Ascomycota; however, the relative abundances of Acidobacteria and Actinobacteria decreased. Redundancy analysis (RDA) and structural equation model (SEM) analysis showed that the bioavailability of heavy metals decreased and that soil physicochemical characteristics improved and had positive or negative effects on the diversity and composition of soil microbial community.

Microbial community analysis of biopiles in Antarctica provides evidence of successful hydrocarbon biodegradation and initial soil ecosystem recovery

Microorganisms comprise the bulk of biodiversity and biomass in Antarctic terrestrial ecosystems. To effectively protect and manage the Antarctic environment from anthropogenic impacts including contamination, the response and recovery of microbial communities should be included in soil remediation efficacy and environmental risk assessments. This is the first investigation into the microbial dynamics associated with large scale bioremediation of hydrocarbon contaminated soil in Antarctica. Over five years of active management, two significant shifts in the microbial community were observed. The initial shift at 12-24 months was significantly correlated with the highest hydrocarbon degradation rates, increased microbial loads, and significant increases in alkB gene abundances. ANCOM analysis identified bacterial genera most likely responsible for the bulk of degradation including Alkanindiges, Arthrobacter, Dietzia and Rhodococcus. The second microbial community shift occurring from 36 to 60 months was associated with further reductions in hydrocarbons and a recovery of amoA nitrification genes, but also increasing pH, accumulation of nitrite and a reduction of oligotrophic bacterial species. Over time, the addition of inorganic fertilisers altered the soil chemistry and led to a disruption of the nitrogen cycle, most likely decoupling ammonia oxidisers from nitrite oxidisers, resulting in nitrite accumulation. The results from this study provide key insights to the long-term management of hydrocarbon bioremediation in Antarctic soils.

Diesel-born organosulfur compounds stimulate community re-structuring in a diesel-biodesulfurizing consortium

We enriched and characterized a biodesulfurizing consortium (designated as MG1). The MG1 consortium reduced the total sulfur of diesel by 25 % and utilized each of the diesel-born compounds dibenzothiophene (DBT), benzothiophene (BT), 4-methyldibenzothiophene (4-MDBT) and 4, 6-dimethyldibenzothiophene (4, 6-DMDBT) as a sole sulfur source. MiSeq analysis revealed compositional shifts in the MG1 community according to the type of the sulfur source. A DBT-grown MG1 culture had Klebsiella, Pseudomonas, Rhodococcus and Sphingomonas as the most abundant genera. When diesel or 4, 6-DMDBT was provided as a sole sulfur source, Klebsiella and Pseudomonas spp. were the most abundant. In the BT culture, Rhodococcus spp. were the key biodesulfurizers, while Klebsiella, Pseudomonas and Sphingomonas spp. dominated the 4-MDBT-grown consortium. MG1 also utilized 2-hydroxybiphenyl (the product of the 4S biodesulfurization pathway) where Pseudomonas spp. uniquely dominated the consortium. The data improves our understanding of the sulfur source-driven structural adaptability of biodesulfurizing consortia.

Effects of co-contamination of heavy metals and total petroleum hydrocarbons on soil bacterial community and function network reconstitution

Due to the accumulation of heavy metals in soil ecosystems, the response of soil microorganisms to the disturbance of heavy metals were widely studied. However, little was known about the interactions among microorganisms in heavy metals and total petroleum hydrocarbons (TPH) co-contaminated soils. In the present study, the microbiota shifts of 2 different contamination types of heavy metal-TPH polluted soils were investigated. NGS sequencing approach was adopted to illustrate the microbial community structure and to predict community function. Networks were established to reveal the interactions between microbes and environmental pollutants. Results showed that the alpha diversity and OTUs number of soil microbiota were reduced under heavy metals and TPH pollutants. TPH was the major pollutant in HT1 group, in which Proteobacteria phylum increased significantly, including Arenimonas genus, Sphingomonadaceae family and Burkholderiaceae family. Moreover, the function structures based on the KEGG database of HT1 group was enriched in the benzene matter metabolism and bacterial motoricity in microbiota. In contrast, severe Cr-Pb-TPH co-pollutants in HT2 increased the abundance of Firmicutes. In details, the relative abundance of Streptococcus genus and Bacilli class raised sharply. The DNA replication functions in microbiota were enriched under severely contaminated soil as a result of high concentrations of heavy metals and TPH pollutants' damage to bacteria. Furthermore, according to the correlation analysis between microbes and the pollutants, Streptococcus, Neisseria, Aeromonas, Porphyromonas and Acinetobacter were suggested as the bioremediation bacteria for Cr and Pb polluted soils, while Syntrophaceae spp. and Immundisolibacter were suggested as the bioremediation bacteria for TPH polluted soil. The study took a survey on the microbiota shifts of the heavy metals and TPH polluted soils, and the microbe's biomarkers provided new insights for the candidate strains of biodegradation, while further researches are required to verify the biodegradation mechanism of these biomarkers.

Uptake and detoxification of diesel oil by a tropical soil Actinomycete Gordonia amicalis HS-11: Cellular responses and degradation perspectives

A tropical soil Actinomycete, Gordonia amicalis HS-11, has been previously demonstrated to degrade unsaturated and saturated hydrocarbons (squalene and n-hexadecane, respectively) in an effective manner. In present study, G. amicalis HS-11 degraded 92.85 ± 3.42% of the provided diesel oil [1% (v/v)] after 16 days of aerobic incubation. The effect of different culture conditions such as carbon source, nitrogen source, pH, temperature, and aeration on degradation was studied. During degradation, this Actinomycete synthesized surface active compounds (SACs) in an extracellular manner that brought about a reduction in surface tension from 69 ± 2.1 to 30 ± 1.1 mN m^-1 after 16 days. The morphology of cells grown on diesel was monitored by using a Field Emission Scanning Electron Microscope. Diesel-grown cells were longer and clumped with smooth surfaces, possibly due to the secretion of SACs. The interaction between the cells and diesel oil was studied by Confocal Laser Scanning Microscope. Some cells were adherent on small diesel droplets and others were present in the non-attached form thus confirming the emulsification ability of this organism. The fatty acid profiles of the organism grown on diesel oil for 48 h were different from those on Luria Bertani Broth. The genotoxicity and cytotoxicity of diesel oil before and after degradation were determined. Cytogenetic parameters such as mitotic index (MI); mitosis distribution and chromosomal aberration (type and frequency) were assessed. Oxidative stress was evaluated by measuring levels of catalase, superoxide dismutase and concentration of malondialdehyde. On the basis of these studies it was deduced that the degradation metabolites were relatively non-toxic.

Microbial Degradation of Hydrocarbons-Basic Principles for Bioremediation: A Review

Crude oil-derived hydrocarbons constitute the largest group of environmental pollutants worldwide. The number of reports concerning their toxicity and emphasizing the ultimate need to remove them from marine and soil environments confirms the unceasing interest of scientists in this field. Among the various techniques used for clean-up actions, bioremediation seems to be the most acceptable and economically justified. Analysis of recent reports regarding unsuccessful bioremediation attempts indicates that there is a need to highlight the fundamental aspects of hydrocarbon microbiology in a clear and concise manner. Therefore, in this review, we would like to elucidate some crucial, but often overlooked, factors. First, the formation of crude oil and abundance of naturally occurring hydrocarbons is presented and compared with bacterial ability to not only survive but also to utilize such compounds as an attractive energy source. Then, the significance of nutrient limitation on biomass growth is underlined on the example of a specially designed experiment and discussed in context of bioremediation efficiency. Next, the formation of aerobic and anaerobic conditions, as well as the role of surfactants for maintaining appropriate C:N:P ratio during initial stages of biodegradation is explained. Finally, a summary of recent scientific reports focused on the removal of hydrocarbon contaminants using bioaugmentation, biostimulation and introduction of surfactants, as well as biosurfactants, is presented. This review was designed to be a comprehensive source of knowledge regarding the unique aspects of hydrocarbon microbiology that may be useful for planning future biodegradation experiments. In addition, it is a starting point for wider debate regarding the limitations and possible improvements of currently employed bioremediation strategies.

Hydrocarbon Removal by Two Differently Developed Microbial Inoculants and Comparing Their Actions with Biostimulation Treatment

Bioremediation of soils polluted with petroleum compounds is a widely accepted environmental technology. We compared the effects of biostimulation and bioaugmentation of soil historically contaminated with aliphatic and polycyclic aromatic hydrocarbons. The studied bioaugmentation treatments comprised of the introduction of differently developed microbial inoculants, namely: an isolated hydrocarbon-degrading community C1 (undefined-consisting of randomly chosen degraders) and a mixed culture C2 (consisting of seven strains with well-characterized enhanced hydrocarbon-degrading capabilities). Sixty days of remedial treatments resulted in a substantial decrease in total aliphatic hydrocarbon content; however, the action of both inoculants gave a significantly better effect than nutrient amendments (a 69.7% decrease for C1 and 86.8% for C2 vs. 34.9% for biostimulation). The bioaugmentation resulted also in PAH removal, and, again, C2 degraded contaminants more efficiently than C1 (reductions of 85.2% and 64.5%, respectively), while biostimulation itself gave no significant results. Various bioassays applying different organisms (the bacterium Vibrio fischeri, the plants Sorghum saccharatum, Lepidium sativum, and Sinapis alba, and the ostracod Heterocypris incongruens) and Ames test were used to assess, respectively, potential toxicity and mutagenicity risk after bioremediation. Each treatment improved soil quality, however only bioaugmentation with the C2 treatment decreased both toxicity and mutagenicity most efficiently. Illumina high-throughput sequencing revealed the lack of (C1) or limited (C2) ability of the introduced degraders to sustain competition from indigenous microbiota after a 60-day bioremediation process. Thus, bioaugmentation with the bacterial mixed culture C2, made up of identified, hydrocarbon-degrading strains, is clearly a better option for bioremediation purposes when compared to other treatments.

Heavy Metals as a Factor Increasing the Functional Genetic Potential of Bacterial Community for Polycyclic Aromatic Hydrocarbon Biodegradation

The bioremediation of areas contaminated with hydrocarbon compounds and heavy metals is challenging due to the synergistic toxic effects of these contaminants. On the other hand, the phenomenon of the induction of microbial secretion of exopolysaccharides (EPS) under the influence of heavy metals may contribute to affect the interaction between hydrophobic hydrocarbons and microbial cells, thus increasing the bioavailability of hydrophobic organic pollutants. The purpose of this study was to analyze the impact of heavy metals on the changes in the metapopulation structure of an environmental consortium, with particular emphasis on the number of copies of orthologous genes involved in exopolysaccharide synthesis pathways and the biodegradation of hydrocarbons. The results of the experiment confirmed that the presence of heavy metals at concentrations of 50 mg·L^-1 and 150 mg·L^-1 resulted in a decrease in the metabolic activity of the microbial consortium and its biodiversity. Despite this, an increase in the biological degradation rate of polycyclic aromatic hydrocarbons was noted of 17.9% and 16.9%, respectively. An assessment of the estimated number of genes crucial for EPS synthesis and biodegradation of polycyclic aromatic hydrocarbons confirmed the relationship between the activation of EPS synthesis pathways and polyaromatic hydrocarbon biodegradation pathways. It was established that microorganisms that belong to the Burkholderiales order are characterized by a high representation of the analyzed orthologs and high application potential in areas contaminated with heavy metals and hydrocarbons.

Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures

The aim of the present study was to reveal how different microbial communities evolve in diesel fuel/crude oil-contaminated environments under aerobic and microaerobic conditions. To investigate this question, aerobic and microaerobic bacterial enrichments amended with a diesel fuel/crude oil mixture were established and analysed. The representative aerobic enrichment community was dominated by Gammaproteobacteria (64.5%) with high an abundance of Betaproteobacteriales (36.5%), followed by Alphaproteobacteria (8.7%), Actinobacteria (5.6%), and Candidatus Saccharibacteria (4.5%). The most abundant alkane monooxygenase (alkB) genotypes in this enrichment could be linked to members of the genus Rhodococcus and to a novel Gammaproteobacterium, for which we generated a high-quality draft genome using genome-resolved metagenomics of the enrichment culture. Contrarily, in the microaerobic enrichment, Gammaproteobacteria (99%) overwhelmingly dominated the microbial community with a high abundance of the genera Acinetobacter (66.3%), Pseudomonas (11%) and Acidovorax (11%). Under microaerobic conditions, the vast majority of alkB gene sequences could be linked to Pseudomonas veronii. Consequently, results shed light on the fact that the excellent aliphatic hydrocarbon degrading Rhodococcus species favour clear aerobic conditions, while oxygen-limited conditions can facilitate the high abundance of Acinetobacter species in aliphatic hydrocarbon-contaminated subsurface environments.

The Heavy-Metal Resistance Determinant of Newly Isolated Bacterium from a Nickel-Contaminated Soil in Southwest Slovakia

A bacterial isolate MR-CH-I2 [KC809939] isolated from soil contaminated mainly by high nickel concentrations in southwest Slovakia was previously found carrying nccA-like heavy-metal resistance determinant, marked as MR-CH-I2-HMR [KF218096]. According to phylogenetic analysis of short (696 bp) 16S rDNA (16S rRNA) sequences this bacterium was tentatively assigned to Uncultured beta proteobacterium clone GC0AA7ZA05PP1 [JQ913301]. nccA-like gene product was on the same base of its partial (581 bp) sequences tentatively assigned to CzcA family heavy metal efflux pump [YP_001899332] from Ralstonia picketii 12J with 99% similarity. In this study the bacterium MR-CH-I2 and its heavy-metal resistance determinant were more precisely identified. This bacterial isolate was on the base of phylogenetic analysis of almost the whole (1,500 bp) 16S rDNA (16S rRNA) sequence, MR-CH-I2 [MF102046], and sequence for gyrB gene and its product respectively, MR-CH-I2-gyrB [MF134666], assigned to R. picketii 12J [CP001068] with 99 and 100% similarities, respectively. In addition, the whole nccA-like heavy-metal resistance gene sequence (3,192 bp), marked as MR-CH-I2-nccA [KR476581], was obtained and on the base of phylogenetic analysis its assignment was confirmed to MULTISPECIES: cation efflux system protein CzcA [WP_004635342] from Burkholderiaceae with 98% similarity. Furthermore, although the bacterium carried one high molecular plasmid of about 50 kb in size, nccA-like gene was not located on this plasmid. Finally, the results from RT-PCR analysis showed that MR-CH-I2-nccA gene was significantly induced only by the addition of nickel.

Metagenomic Analysis of Soil Bacterial Community and Level of Genes Responsible for Biodegradation of Aromatic Hydrocarbons

The aim of the studies was to compare the composition of soil bacterial metabiomes originating from urbanized areas and areas con¬taminated with hydrocarbons with those from agricultural soil and forest soil obtained from a protected wild-life park area. It should be noted that hydrocarbons are everywhere therefore bacteria capable of their utilization are present in every soil type. In the hydrocarbon-contaminated soil and in the soil of anthropogenic origin, the bacteria belonging to Gammaproteobacteria were dominant (28.4-36.6%), whereas in the case of agricultural soil and protected wild-life park soil their ratios decreased (22.8-23.0%) and were similar to that of Alphaproteobacteria. No statistically significant changes were observed in terms of the Operational Taxonomic Unit identified in the studies soils, however, based on the determined alpha-diversity it can be established that contaminated soils were characterized by lower biodiversity indices compared to agricultural and forest soils. Furthermore, the dioxygenase level was also evaluated in the studied soils, which are genes encoding crucial enzymes for the decomposition of mono- and polycyclic aromatic hydrocarbons during the biodegradation of diesel oil (PAHRHDαGN, PAHRHDαGP, xylE, Cat 2,3, ndoB). It was concluded that both the population structure of the soil metabiome and the number of genes crucial for biodegradation processes differed significantly between the soils. The level of analysed genes showed a similar trend, as their highest number in relations to genes encoding 16S RNA was determined in urban and hydrocarbon-contaminated soil.

Immobilization of cadmium and improvement of bacterial community in contaminated soil following a continuous amendment with lime mixed with fertilizers: A four-season field experiment

The effects of the continuous amendments with lime (L), lime mixed with organic manure (LO), or phosphate fertilizer (LP) on the soil bacterial community, soil available cadmium (Cd) content, and Cd accumulation in rice planted in a Cd contaminated paddy soil were determined through a four-season field experiment. The results showed that with continuous application of amendments during the four seasons, the soil pH increased significantly compared with the control, while the soil available Cd content significantly decreased by 12.9-18.2%, 13.1-17.3% and 0.09-23.2% under the L, LO, or LP treatments, and the Cd content of rice was significantly reduced by 28.5-56.2%, 37.6-53.4%, and 31.2-44.6%, respectively. The rice Cd content in each season at amendment treatments was lower than the National Food Safety Standard of China (maximum level of Cd in grains is 0.2 mg/kg). The diversity and richness of soil bacteria significantly increased after the continuous amendments in soil for four-season cropping. Soil pH and available Cd content were important factors for soil bacterial community. Lime mixed with phosphate fertilizer or organic manure had been characterized by a significant increase of Proteobacteria, Nitrospirae, and Chloroflexi and a decrease of Acidobacteria based on an Illumina Miseq sequencing analysis. The results indicate that the continuous application of lime mixed with organic manure or phosphate fertilizer is a very important measure to ensure the quality safety of rice and improve soil quality in a Cd-contaminated paddy.

Hydrocarbonoclastic Ascomycetes to enhance co-composting of total petroleum hydrocarbon (TPH) contaminated dredged sediments and lignocellulosic matrices

Four new Ascomycete fungi capable of degrading diesel oil were isolated from sediments of a river estuary mainly contaminated by shipyard fuels or diesel oil. The isolates were identified as species of Lambertella, Penicillium, Clonostachys, and Mucor. The fungal candidates degraded and adsorbed the diesel oil in suspension cultures. The Lambertella sp. isolate displayed the highest percentages of oxidation of diesel oil and was characterised by the capacity to utilise the latter as a sole carbon source. This isolate showed extracellular laccase and Mn-peroxidase activities in the presence of diesel oil. It was tested for capacity to accelerate the process of decontamination of total petroleum hydrocarbon contaminated sediments, co-composted with lignocellulosic residues and was able to promote the degradation of 47.6% of the TPH contamination (54,074 ± 321 mg TPH/Kg of sediment) after two months of incubation. The response of the bacterial community during the degradation process was analysed by 16S rRNA gene meta-barcoding.

Comparison of Petroleum Hydrocarbons Degradation by Klebsiella pneumoniae and Pseudomonas aeruginosa

: The aim of this work was to develop bacterial communities to effectively degrade petroleum hydrocarbons (PHs). We investigated the biotic and abiotic contributors to differences in PHs degradation efficacy between two bacterial strains, Klebsiella pneumoniae (Kp) and Pseudomonas aeruginosa (Pa), screened out from the activated sludge of a petroleum refinery. We characterized the temporal variations in degradation efficacy for diesel and its five major constituents as a sole carbon source and identified more constituents they degraded. The growth characteristics, surface tension, hydrophobicity and emulsifiability of these two strains were measured. We further estimated the relationships between their degradation efficacy and all the biotic and abiotic factors. Results showed that the Pa strain had higher diesel degradation efficacy (58% on Day 14) and utilized more diesel constituents (86%) compared to Kp. Additionally, the growth of the Pa strain in diesel medium was faster than that of the Kp strain. The Pa strain had a lower surface tension and higher hydrophobicity and emulsifiability than Kp, while the surfactant produced by Pa was identified as rhamnolipids. Degradation of PHs was positively related to bacterial growth, hydrophobicity and emulsification but negatively related to surface tension. Overall, differences in degrading capacity for diesel constituents, relative growth rate, and biosurfactant production contributed to the variation in the PHs degradation efficacy of these two bacterial strains.

Natural Attenuation Potential of Polychlorinated Biphenyl-Polluted Marine Sediments

The marine environment in Kuwait is polluted with various hazardous chemicals of industrial origin. These include petroleum hydrocarbons, halogenated compounds and heavy metals. Bioremediation with dedicated microorganisms can be effectively applied for reclamation of the polluted marine sediments. However, information on the autochthonous microbes and their ecophysiology is largely lacking. We analyzed sediments from Shuwaikh harbor to detect polychlorinated biphenyls (PCBs) and total petroleum hydrocarbons (TPHs). Then we adopted both culture-dependent and culture-independent (PCR-DGGE) approaches to identify bacterial inhabitants of the polluted marine sediments from Shuwaikh harbor. The chemical analysis revealed spatial variation among the sampling stations in terms of total amount of PCBs, TPHs and the PCB congener fingerprints. Moreover, in all analyzed sediments, the medium-chlorine PCB congeners were more abundant than the low-chlorine and high-chlorine counterparts. PCR-DGGE showed the presence of members of the Proteobacteria, Spirochaetes, Firmicutes and Bacteroidetes in the analyzed sediments. However, Chloroflexi-related bacteria dominated the detected bacterial community. We also enriched a biphenyl-utilizing mixed culture using the W2 station sediment as an inoculum in chemically defined medium using biphenyl as a sole carbon and energy source. The enriched mixed culture consisted mainly of the Firmicute Paenibacillus spp. Sequences of genes encoding putative aromatic ring-hydroxylating dioxygenases were detected in sediments from most sampling stations and the enriched mixed culture. The results suggest the potential of bioremediation as a means for natural attenuation of Shuwaikh harbor sediments polluted with PCBs and TPHs.

Biodiversity of soil bacteria exposed to sub-lethal concentrations of phosphonium-based ionic liquids: Effects of toxicity and biodegradation

Little is known about the effect of ionic liquids (ILs) on the structure of soil microbial communities and resulting biodiversity. Therefore, we studied the influence of six trihexyl(tetradecyl)phosphonium ILs (with either bromide or various organic anions) at sublethal concentrations on the structure of microbial community present in an urban park soil in 100-day microcosm experiments. The biodiversity decreased in all samples (Shannon's index decreased from 1.75 down to 0.74 and OTU's number decreased from 1399 down to 965) with the largest decrease observed in the microcosms spiked with ILs where biodegradation extent was higher than 80%. (i.e. [P₆₆₆₁₄][Br] and [P₆₆₆₁₄][2,4,4]). Despite this general decrease in biodiversity, which can be explained by ecotoxic effect of the ILs, the microbial community in the microcosms was enriched with Gram-negative hydrocarbon-degrading genera e.g. Sphingomonas. It is hypothesized that, in addition to toxicity, the observed decrease in biodiversity and change in the microbial community structure may be explained by the primary biodegradation of the ILs or their metabolites by the mentioned genera, which outcompeted other microorganisms unable to degrade ILs or their metabolites. Thus, the introduction of phosphonium-based ILs into soils at sub-lethal concentrations may result not only in a decrease in biodiversity due to toxic effects, but also in enrichment with ILs-degrading bacteria.